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Hello everyone! I'm trying to run a `test_full` of...
# oncoanalyser
b
Hello everyone! I'm trying to run a 
test_full
of oncoanalyser version 2.2.0 but 
READ_ALIGNMENT_DNA:BWAMEM2_ALIGN
fails with no specific error (see error log in thread). So I was wondering, is this a known issue that was patched in the latest version? Couldn't find anything in the repository or documentation. It ran with 
-profile test_full,singularity
and the following parameters:
Copy code
mode: wgts
genome: GRCh38_hmf
create_stub_placeholders: false
Copy code
Command error:
  Executing in AVX512 mode!!
  -----------------------------
  * SA compression enabled with xfactor: 8
  * Ref file: GRCh38_masked_exclusions_alts_hlas.fasta
  * Entering FMI_search
  * Index file found. Loading index from GRCh38_masked_exclusions_alts_hlas.fasta.bwt.2bit.64
  * Reference seq len for bi-index = 6434704607
  * sentinel-index: 2734639315
  * Count:
  0,    1
  1,    1876948439
  2,    3217352304
  3,    4557756169
  4,    6434704607

  * Reading other elements of the index from files GRCh38_masked_exclusions_alts_hlas.fasta                                                                                                    [23/1806]
  * Index prefix: GRCh38_masked_exclusions_alts_hlas.fasta
  * Read 0 ALT contigs
  * Done reading Index!!
  * Reading reference genome..
  * Binary seq file = GRCh38_masked_exclusions_alts_hlas.fasta.0123
  * Reference genome size: 6434704606 bp
  * Done reading reference genome !!

  ------------------------------------------
  1. Memory pre-allocation for Chaining: 1393.3971 MB
  2. Memory pre-allocation for BSW: 2875.4043 MB
  3. Memory pre-allocation for BWT: 927.7701 MB
  ------------------------------------------
  * Threads used (compute): 12
  * No. of pipeline threads: 2

  [0000] read_chunk: 100000000, work_chunk_size: 63043794, nseq: 420292
        [0000][ M::kt_pipeline] read 420292 sequences (63043794 bp)...
  [0000] Calling mem_process_seqs.., task: 0
  [0000] 1. Calling kt_for - worker_bwt
  [0000] read_chunk: 100000000, work_chunk_size: 0, nseq: 0
  [0000] 2. Calling kt_for - worker_aln
  [0000] Inferring insert size distribution of PE reads from data, l_pac: 3217352303, n: 420292
  [0000][PE] # candidate unique pairs for (FF, FR, RF, RR): (0, 194474, 0, 0)
  [0000][PE] skip orientation FF as there are not enough pairs
  [0000][PE] analyzing insert size distribution for orientation FR...
  [0000][PE] (25, 50, 75) percentile: (492, 499, 506)
  [0000][PE] low and high boundaries for computing mean and std.dev: (464, 534)
  [0000][PE] mean and std.dev: (498.97, 10.16)
  [0000][PE] low and high boundaries for proper pairs: (450, 548)
  [0000][PE] skip orientation RF as there are not enough pairs
  [0000][PE] skip orientation RR as there are not enough pairs
  [0000] 3. Calling kt_for - worker_sam
        [0000][ M::mem_process_seqs] Processed 420292 reads in 63.435 CPU sec, 5.536 real sec
r
Hi Beatriz, can you give more details please ? Like the executor you're using - I have not seen any issues with bwa-mem2, in 2.2.0 or since
b
Hi @Rayan Hassaïne! I just ran it locally, in an HPC with Linux OS and with 
nextflow version 25.10.4.11173
. Is there any more information that would be helpful?
r
what scheduler are you using ? slurm, lsf, etc ? Or did you run directly in a powerful VM ?
b
Yeah, no scheduler or executor, just directly in one of the compute nodes.
r
Hmmm, odd - I know that on some HPCs, that's not "allowed" and then the system kills the run automatically, especially if it uses too much compute
👍 1
and when an external system kills, the logging is very minimal, you're not told much
could you try to submit as a job to see if that fixes things perhaps ?
b
Oh that could be an issue! I will try it out and possibly adjust memory allocation and so now. Thank you so much for your help @Rayan Hassaïne!
🙏 1
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